Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Damian Rafal Plichta; Agnieszka Sierakowska Juncker; Marcelo Bertalan; Elizabeth Rettedal; Laurent Gautier; Encarna Varela; Chaysavanh Manichanh; Charlène Fouqueray; Florence Levenez; Trine Nielsen; Joël Doré; Ana Manuel Dantas Machado; Mari Cristina Rodriguez de Evgrafov; Torben Hansen; Torben Jørgensen; Peer Bork; Francisco Guarner; Oluf Pedersen; Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium; Morten O A Sommer; S Dusko Ehrlich; Thomas Sicheritz-Pontén; Søren Brunak; H Bjørn Nielsen

doi:10.1038/nmicrobiol.2016.152

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Damian Rafal Plichta, Agnieszka Sierakowska Juncker, Marcelo Bertalan, Elizabeth Rettedal, Laurent Gautier, Encarna Varela, Chaysavanh Manichanh, Charlène Fouqueray, Florence Levenez, Trine Nielsen, Joël Doré, Ana Manuel Dantas Machado, Mari Cristina Rodriguez de Evgrafov, Torben Hansen, Torben Jørgensen, Peer Bork, Francisco Guarner, Oluf Pedersen, Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Morten O A SommerS Dusko Ehrlich, Thomas Sicheritz-Pontén, Søren Brunak, H Bjørn Nielsen

29 Citations (Scopus)

Abstract

The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species(1). Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect functional and metabolic interactions between cohabiting species(2,3). To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from Europeans. In 102 significantly interacting species pairs, the transcriptional changes led to a reduced expression of orthologous functions between the coexisting species. Specific species-species transcriptional interactions were enriched for functions important for H2 and CO2 homeostasis, butyrate biosynthesis, ATP-binding cassette (ABC) transporters, flagella assembly and bacterial chemotaxis, as well as for the metabolism of carbohydrates, amino acids and cofactors. The analysis gives the first insight into the microbial community-wide transcriptional interactions, and suggests that the regulation of gene expression plays an important role in species adaptation to coexistence and that niche segregation takes place at the transcriptional level.

Original language	English
Article number	16152
Journal	Nature Microbiology
Volume	1
Pages (from-to)	1-6
Number of pages	6
ISSN	2058-5276
DOIs	https://doi.org/10.1038/nmicrobiol.2016.152
Publication status	Published - 26 Aug 2016

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Plichta, D. R., Juncker, A. S., Bertalan, M., Rettedal, E., Gautier, L., Varela, E., Manichanh, C., Fouqueray, C., Levenez, F., Nielsen, T., Doré, J., Machado, A. M. D., de Evgrafov, M. C. R., Hansen, T., Jørgensen, T., Bork, P., Guarner, F., Pedersen, O., Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, ... Nielsen, H. B. (2016). Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nature Microbiology, 1, 1-6. [16152]. https://doi.org/10.1038/nmicrobiol.2016.152

Plichta, DR, Juncker, AS, Bertalan, M, Rettedal, E, Gautier, L, Varela, E, Manichanh, C, Fouqueray, C, Levenez, F, Nielsen, T, Doré, J, Machado, AMD, de Evgrafov, MCR, Hansen, T, Jørgensen, T, Bork, P, Guarner, F, Pedersen, O, Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Sommer, MOA, Ehrlich, SD, Sicheritz-Pontén, T, Brunak, S & Nielsen, HB 2016, 'Transcriptional interactions suggest niche segregation among microorganisms in the human gut', Nature Microbiology, vol. 1, 16152, pp. 1-6. https://doi.org/10.1038/nmicrobiol.2016.152

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AU - Gautier, Laurent

AU - Varela, Encarna

AU - Manichanh, Chaysavanh

AU - Fouqueray, Charlène

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AU - Nielsen, Trine

AU - Doré, Joël

AU - Machado, Ana Manuel Dantas

AU - de Evgrafov, Mari Cristina Rodriguez

AU - Hansen, Torben

AU - Jørgensen, Torben

AU - Bork, Peer

AU - Guarner, Francisco

AU - Pedersen, Oluf

AU - Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium

AU - Sommer, Morten O A

AU - Ehrlich, S Dusko

AU - Sicheritz-Pontén, Thomas

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AU - Nielsen, H Bjørn

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Transcriptional interactions suggest niche segregation among microorganisms in the human gut

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